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  1. Jul 2019
    1. Estimation of bioaccumulation of trace metals inmuscle and gill tissue of fish, Labeo rohita
  2. Jun 2019
    1. concentrators (Amicon), and subjected to reduction with 0.0.5 M sodium dithionite. For this an appropriate amount of anaerobically prepared dithionite solution was added to the reconstituted Hb and the reaction mixture was quickly passed through a Sephadex G25 gel filtration column (30 em x 1.5 em) equilibrated with 0.05 M Tris HCI (pH 7.4), in order to minimize the duration of contact of dithionite with the protein. The reduced Hb was dialyzed extensively against 0.01 M potassium phosphate buffer (pH 6.5) and loaded onto a CM52 column (1 Ocm x 1.5cm) equilibrated with the same buffer. A linear gradient of 150 ml each of 0.01 M potassium phosphate buffer (pH 6.5) and 0.015 M potassium phosphate buffer (pH 8.5) was employed to elute the protein from the column
    2. Construction of mutant a globins
    3. Reconstitution of a globin and rf chain into HbS tetramers
  3. May 2019
    1. appropriate secondary antibody (conjugated with horse-radish peroxidase) diluted in 5% fat free milk solution (in PBST) and incubated for 45 minutes at room temperature. After incubation the membrane was washed and processed for the detection of protein bands using ECL-plus detection reagent (Amersham Biosciences) followed by detection of signal on X-ray film (Hyperfilm-ECL, Amersham Biosciences)
    2. The proteins were resolved using denaturing SDS-PAGE gel and after completion of the run, the gel was over laid on a nitrocellulose paper cut to the size of gel and kept in the blotting cassette in the presence of blotting buffer. Finally the cassette was put in the mini transblot apparatus (Bio Rad) and blotting was done for 4 hours at a constant voltage of 60 V. Then the membrane was taken out and rinsed in PBS containing 0.1% Tween - 20 (PBST) for 5 minutes by gentle shaking. Later the membrane was immersed in 5% non-fat milk solution in PBST with gentle shaking for 1 hour at 37°C. The membrane was washed off from the traces of the fat free milk with PBST and the membrane was over laid with primary antibody diluted in PBST for 3 hours at 4°C with shaking. After incubation the membrane was washed with PBST and layered with
    3. Immunobloting
    1. f. 5 μl of water was then spotted on each spot for 30 sec and removed using Whatman filter paper strips. This step was repeated once. g. 1-2 μl of SAP matrix was then applied to each spot and allowed to dry. h. The chip was then placed in the SELDI machine
    2. a. 5 μl of 10 mM HCl was added to each spot on the chip and removed after 5 min. using Whatman filter paper strips. b. Washing was given by spotting 3 μl of water for 30 sec on each spot followed by removal using Whatman filter paper strips. This step was repeated two times. c. 10 μl of low stringency/ high stringency buffer was then added to the spot and kept in humid chamber for 5 min. followed by removal using Whatman filter paper strips. d. 3 μl of sample prepared in low stringency/ high stringency buffer was then added to the spot and incubated in humid chamber for 30 min. e. Washed the spot with 5 μl of low stringency buffer/ high stringency buffer/ buffer of pH 3.0/ pH 5.0/ pH 7.0 for 30 sec and removed using Whatman filter paper strips. This step was repeated five times.
    3. Activation of CM10 (weak cation exchange ) array
    4. Fresh overnight culture of the E. coli strain (DH5α) was subcultured 1:100 in 250 ml LB/SOB media at 18 ̊C and 2500g and allowed to grow to an A600=0.55. Culture was chilled on ice and centrifuged at 2500g at 4 ̊C for 10 min. The cell pellet was redissolved in 80 ml ice-cold Inoue transformation buffer (55 mM MnCl2, 15 mM CaCl2, 250 mM KCl, 10 mM PIPES pH6.7). This cell suspension was centrifuged at 2500g at 4 ̊C for 10 min. and the cell pellet was resuspend in 20ml ice-cold Inoue buffer with 1.5 ml DMSO. This mixture was then placed on ice for 10 min. Aliquots of this suspension were dispensed into chilled, sterile microfuge tubes that were snap-frozen in a bath of liquid nitrogen. Tubes were stored at ─70 ̊C until required. For transformation the cells were thawed on ice and plasmid DNA was added followed by the standard transformation protocol
    5. Preparation of ultracompetent cells
    1. Band intensities in gel autoradiograms were determined by densitometry with the aid of the Fujifilm Multi Gauge V3.0 imaging system.Equal areas of radioactive bands (preferably the unbound probe) were boxed and the PSL (Photostimulated luminescence) valueswere further considered. For Kd(dissociation constant)calculations, the values thus obtained for each lane were expressed as a percentage with respect to the PSL for the lane without any protein taken as 100%
    2. Densitometry
    1. Plasma membrane H+-ATPase activitywas measured inthe total membrane fraction as described previously (Nakamura et al., 2001).5μg totalmembrane fraction was incubated at 30 ̊C in 120 μl reaction buffer containing 10 mM MgSO4and 50 mM KCl in 50 mM MES (pH 5.7) with 5mM adenosine tri-phosphate (ATP). To eliminate possible contribution of residual ATPases, viz.,vacuolar ATPases, mitochondrial ATPases or non-specific phosphatases, 50mM KNO3, 5mM NaN3and 0.2mM ammonium molybdate were used, respectively, in the assay mixture. Reaction was stoppedafter 30 minby adding 130μl stop-developing solution containing 1% (w/v) SDS, 0.6M H2SO4, 1.2%(w/v)ammonium molybdate and 1.6%(w/v) ascorbic acid. Amount of inorganic phosphate (Pi) liberated was measured at A750nmafter 10 minincubation at room temperature. A standard curve prepared with0-50 μmolesof KH2PO4 was used fordetermination of total Piamount.ATPase activity of the plasma membrane was expressed in micromoles of Pireleased per milligram protein per min. ATPase activity was also determined in the presence of plasma membrane H+-ATPase inhibitor diethylstilbestrol (DES,Sigma# D4628),wherein total membrane fraction was incubated with 0.2mM DES for 5 min, prior to the enzymatic measurement
    2. Plasma membrane H+-ATPase activity assay
    3. dithiothreitol and1X protease inhibitor cocktail. Cell suspension was rapidly frozen at -80 ̊C,thawed and lysed with 0.5mm acid-washed glass beadsin a homogenizer (FastPrep®-24,MP Biomedicals)at maximum speed of 60 secfive times. Homogenate wasdiluted with 5mlTris-HCl (0.1M; pH 8.0)solutioncontaining 0.33M sucrose, 5mM EDTAand 2mM dithiothreitoland centrifuged at 1,000g for 3 minat 4 ̊C. Supernatant was collected and centrifuged again at 3,000g for 5 minat 4 ̊C to remove unbrokencells. The resulting supernatant was centrifuged at 19,000g for 45 minat 4 ̊C to obtain total membrane fraction. Total membrane pellet was resuspendedin 100μl membrane suspension buffer and stored at -80 ̊Ctill further use. Total protein concentration in the membrane fraction was estimated using BCAprotein assay kit (Thermo Scientific, US) with bovine serum albumin (BSA) used as astandard
    4. Isolation of total membrane fractions from C. glabratastrains were carried out as described previously (Fernandes et al., 1998). Cells grown to log-phase under different environmental conditionswere harvested, washed and suspended to afinal density of 20 OD600cells in 1 ml solution containing100mM Tris (pH 10.7),5mM EDTA,2mM
    5. Total membrane preparation
    6. To assess the activity of plasma membrane proton pump, CgPma1, in cells grown in differentexternal pH environment,whole cell acidification assaywas carried out.This assay is a measurement of glucose-responsive proton pump activityin live cellsand is based on a decrease inthe pH of a weakly-buffered solutionupon extrusion of H+ions from thecell. The amount of change in the pH of the medium represents a crude measurement of the activity of functional plasma membrane proton pump in live cells. Whole cell acidification assay was conductedwithcellsgrown in YNB pH 5.5 and YNB pH 2.0medium as described previously (Martinez-Munoz and Kane, 2008) with slight modifications.After growth at30 ̊C for 2 h, cells were harvested, washed and resuspended(1.5-3.0 mg wet weight/ml) in 15ml MES/TEA (1mM; pH 5.0) buffer. Cell suspension was kept at 25 ̊C with continuousagitation. Extracellular pH of the buffer solution was recorded at 1 mininterval for 20 minwith the help of a pH meter(BT-600, BoecoGermany). To activate plasma membrane proton pumping, glucose and KCl were added to a final concentration of 40mM after 3 and 8 minincubation, respectively. Plasma membrane proton pump activitywas plotted as a change in the pH of the extracellular solutionversustime
    7. Whole cell acidification assay
    8. Measurement of plasma membrane H+-ATPase activity
    9. A single colony of E.coliBW23473strainfrom a freshly-streaked LBplate was inoculated in50ml LB medium. Culture was incubated overnight at 37°C with shaking at 200rpm. 25ml of the overnight-grown BW23473 culturewas transferred to500ml pre-warmed LB medium andincubated at 37°C till the OD600reached to 0.4. After incubation, cultureswere transferred to an ice-water bathandcentrifugeat 1,000g for 15 minat 4°C. Cells were washed twice with 500ml ice-coldwater, thrice with250ml ice-cold 10% glycerol solution and resuspendedin 1ml 10% glycerol solution. Cell suspension wasnormalized to final cell densityof 3x 1010cells/ml and dispensed in 50μl volume into sterile ice-cold microcentrifuge tubes. Aliquots weresnap frozen inliquid nitrogen and stored at -70 ̊C for further use
    10. Electro-competentcell preparation
    11. 5-10 ml saturated bacterial culture harboring the desired plasmid was harvested at 5,000 g for 3 min. Plasmid DNAwas isolated using QIAprep Spin Miniprep Kit (Qiagen, USA) or GenElute™ HP Plasmid Miniprep kit (Sigma-Aldrich, USA) as per manufacturer’s instructions
    12. Bacterial plasmid isolation
    1. temperature. Genomic DNA pellet was dissolvedeitherin 50 μl 0.1X TE or molecular biology grade water containing 0.3 μlAmbion RNAse cocktail and incubated at 37ºC for 30 min.After RNA digestion, 100 μl of 0.1X TE or nuclease-free water was added to the tube and stored at -20ºC. Quality of extracted genomic DNA was checkedon 0.6% agarosegel by electrophoresis
    2. Desired C. glabratastrain wasgrownovernight in YPD liquid medium and yeast cells were harvested by centrifugation at 2,500g in 15 ml polypropylene tube.Yeast cells were washed with PBS, resuspendedin 500μl lysis buffer (Buffer A) andwere transferred toa2ml microcentrifuge tube. Yeast cells were incubated for 15 minon a thermomixer set at 65 ̊C and 750 rpm. After incubation, 0.5 gm glass beads (0.5 mm) and 500 μl PCI solution were added to thetube. Yeast cells were lysedthree times for 45 seconds each on a bead beating apparatus with intermittent cooling on ice to prevent overheating. Cell lysates were centrifugedat 7,500gfor 5 minandupperaqueous phase (300-350 μl) wastransferred carefully to a new 1.5 ml microcentrifuge tube. 1 mlabsolute ethanol was added andmixedwellby inverting the tube3-4 times. To precipitate genomic DNA, suspension was centrifuged at 7,500g for 10min.Precipitated genomic DNA was washedwith 70% ethanolanddried at room
    3. Genomic DNA isolationby glass bead lysis method
    4. For opsonization,C. glabratacells were incubatedwith 1 μg/μl human IgG for 30 min at 37°C and washed thrice with PBS. Alternatively, yeast cells were incubated with 25% human serum at 37°C for 30 min followed by threePBS washes
    5. Opsonizationof C. glabratacells
    6. undertissueculture conditionsfor 45-60min andfixed in 3.7% formaldehydeas described earlier.For DAPI staining, Vectashield mounting medium containing DAPI was used and slides were visualized under confocal microscope.For heat killing, yeast cells were harvested from 1 ml culture, washed, resuspended inPBS andwere incubated at 95°C for 5 min
    7. PMA-treated THP-1 macrophages were infected with C. glabratacells to a MOIof 1:1 in four-chambered slides and incubated at 37°C and 5%CO2. After 1 hcoincubation, each chamber was washed thrice with PBS to eliminate extracellular yeast cellsand medium was replaced with fresh prewarmed RPMI medium containing100 nM Lysotracker Red DND-99.Infected THP-1 macrophageswere incubated
    8. Lysotracker staining
    1. Themixture is incubated in a water bath at 37⁰C for 15 min and afterwards transferred on ice and 4μl of DNA loading buffer is added. The samples were then run on a polyacrylamide gel electrophoresis which had been pre-run for 30 min. Electrophoresis was carried out at 4⁰C for 3h till the bromophenol blue migrated to 2cm above the bottom of gel. The gel was taken out and kept on Whatman filter paper sheet and covered by saran wrap followed by drying in a gel dryer at 80⁰C for 1h under suction. The dried gel was exposed to phosphoimager screen by keeping in phosphoimager cassette overnight
    2. A binding reaction mixture was prepared by adding the following components to a microcentrifuge tube on ic
    3. Binding reaction
    4. The reaction was carried out by incubating at 37⁰C for 30 min. The reaction was stopped by adding 2μl of 0.5M EDTA, pH 8.0 and keeping on ice. A spin column was prepared using 1ml syringe and packed with sterile Sephadex G50 slurry and reaction mixture is applied on the top. The eluate is collected in different microcentrifuge tubes and radioactivity was counted using Geiger counter. The tube showing 7 to 9X106was used for experiment. The column containing the unincorporated [γ-32P] ATP was discarded in radioactive waste bin. The radiolabelled oligonucleotides were annealed with their corresponding complementary unlabelled oligonucleotides. A 50 fold molar excess of the latter was used for annealing for conversion of labelled single strand to double strand. Thetubes were kept in boiling waterbath for 3 min followed by room temperature for 30 min. The tubes were transferred to ice and the oligonucleotides were diluted to 4fmoles/μl using sterile H2O
    5. The oligonucleotides were labelled at their 5'end with 32P using T4 polynucleotide kinase (T4 PNK) enzyme in a reaction given belo
    6. end labelling of the oligonucleotides
    7. Electrophoretic mobility shift assay
    1. in 5% fat free milk solution in TBST (1:7000) for 45 min at room temperature and then washed thrice.The detection of signal was performed with ECL detection reagent (Amersham Biosciences) followed by detection of signal either on X-ray film (Hyperfilm-ECL, Amersham Biosciences)or in a chemidoc system (Proteinsimple, California, USA).The blot was reprobed with anti-tubulinor anti-GAPDHantibody to ensure equal loading of extracted protein
    2. Materials and Methods472.2.7 Estimationof protein concentration in cellular lysatesBradford method(Bradford, 1976)was used to determine the quantity of protein in various samplesin a 96-well plate. Bradford’s reagent was prepared by diluting Bradford dye with water in the ratio of 1:5.For estimating the concentration of protein in a particular sample, 50μl volume reactionwas set and200μl of freshly prepared Bradford’s reagent was added. The complex givesa purplish colorwhose intensity is proportional to the amount of protein present in the sample. A standard curve was also generated using increasing concentrations of BSA (50 μg/ml, 100 μg/mland 200μg/ml).Cell lysatesof test samples werediluted to1:50 in the same volume.Each sample (including blank and standards) was taken in duplicates.The concentration of protein was measuredusing the ELISA reader at 570 nm. The unknown protein concentration (X) was calculated as follows:where,OD1& OD2: Optical densities of Standard (Std) 1 & Standard (Std) 2, respectively.BSA: Bovine serum albuminX×50 (dilution factor)/1000 = YConcentration of unknown protein (μg/μl) = Y × OD2.2.8 Immunoblotting(Western Blotting)Immunoblotting was performed as essentailly described by Lee (Lee, 2007). Equal amounts of protein were resolved on a denaturating SDS-polyacrylamide gel (8-12%). After completion of the run, the gel was transferred onto PVDF membrane and placed in the blotting cassette. The cassette wasthenput intothe mini transblot apparatus and transfer was done for 2-3 hours at a constant voltage of 80 V, depending on the size of the protein. Post transfer, membrane was rinsed in TBS containing 0.1% Tween-20 (TBST) and blocked with 5% non-fat milk in TBST for 1 h at 37ºC,on a gentle shaking rotator. After blocking, membrane wasrinsed thrice in TBST and incubated with primary antibodydiluted in TBST (ranging from 1:1000 to 1:10000, depending upon antibody used) for either3h at room temperature or overnight in the cold room.The membrane was then washed thrice with TBST and incubated withhorseradish peroxidase(HRP)-conjugated secondary antibody diluted
    3. Immunoblotting(Western Blotting)
    1. Yeast were grown till mid-log phase 0.6-0.8 OD600in an appropriate medium and 10 mL of culture was pelleted at 2500 x g. Cells were suspended in 350μLof AEbuffer,mixed with 50μLof 10% sodium dodecyl sulphate and 400μLacid phenol(pH4.3) and immediately shaken vigorously on a dry bath (Eppendorf)at 65°C for 15 min.The tube was then quickly chilled on iceand centrifuged at 12000 x gfor 15 min to separate the aqueous phase from the phenol. After centrifugation, the aqueous phase was transferred to a new tube and extracted with an equal volume of chloroform.RNA was precipitated by adding 50 μLof 3 M sodium acetate (pH 5.3) and equal volume of 100% ethanol followed by incubation at -20°C for 2 h, andcentrifugation at maximum speed for 30 min at 4°C. The pellet obtained was washed in 70% ethanol, dried at room temperature anddissolved in an appropriate volume of DEPC-treated water. The concentration of RNA was estimated by measuring A260using a Nano Drop Spectrophotometer (ND1000). To monitor different classes of rRNA levels, 10 μg of total RNA from each strain was resolved on a 1.2% formaldehyde-agarose gel
    2. RNA extraction by hot-phenol method
    1. final supernatant, beads were boiled in the equal volume of 2X SDS loading buffer (Lamelli Buffer) for 5 min. at 95°C. Bound protein complexes were collected by brief centrifugation (1 min.) at 14000 RPM and the supernatant containing the eluted protein fraction was resolved in SDS gel and analyzed by western blotting technique. For denaturing immunoprecipitation, cells were harvested in 1X PBS andpelleted. Cell pellet was resuspended in denaturing lysis buffer (50mM Tris-HCL, 100mM β-mercaptoethanol, 1% SDS, 5mM EDTA,0.5mM PMSF, 1 mg/ml aprotinin and 1 mg/ml pepstatin) (200μl for 100mm culture dish) and boiled for 10 min at 99°C. Cells suspensionwas briefly sonicated. Ice-cold 1X NETN (800μl) was added to the suspension after sonication and incubated on ice for 20min.,cells were centrifuged at 14000 rpm for 10 min. The supernatant was collected and used for immunoprecipiation by following the standard protocol
    2. Protein-A or protein G beads (50 μl of 50% agarose beads) were washed twice with NETN lysis buffer. 2-5 μg of specific antibody was added to beads (in 1ml NETN) and were incubated with beads for 1 h at 4°C on a rotary shaker. Beads were collected by spinning at 500 g for 2 min.and supernatant was removed. 200-600 μg of totalprotein (mammalian cell lysate or bacterial cell lysate) was added to the beads and incubated for 2 hrs at 4°C on a rotary shaker. Beads were washed four times with the lysis buffer, each time by centrifuging at 500 g for 2 min at 4°C. After discarding the
    3. Immunoprecipitation
    1. ForEPS isolation,X. oryzaepv. oryzicolastrains were plated on PS agar plateand incubated at 28°C. Bacterial lawn was dissolved in 15 ml 1X PBS and 100 μl formamide, and centrifuged at 12,000 g for 6-8 min at RT. Before centrifugation, 1 ml cell suspension was diluted, and plated to get the CFUs. For EPS precipitation, 250 ml chilled acetone was added to the supernatant, and kept at 4°C for overnight (Dharmapuri and Sonti, 1999). EPS was pelleted down at 7000 g for 10 min at 4°C, washed with 10 ml acetone, and kept for drying. After drying, it was dissolved in appropriate volume of water, and quantitated by colorimetric method for estimation of pentoses and hexoses by phenol-sulphuric acid method (Dharmapuri and Sonti, 1999)
    2. EPS isolation and estimation
    3. For DNA precipitation after digestion, 500 μl nuclease free water was added to the digested DNA fragment. Equal volume of phenol:chloroform:isoamyl alcohol (25:24:1) was added to the mixture and centrifuged at 13,000 g for 10 minat RT. Upper aqueous phase containing DNA fragment was transferred to fresh microcentrifuge tube and DNA was precipitated by adding 0.7 volume of iso-propanol and 1/10thvolume of sodium acetate. Precipitated DNA was washed with 70% ethanol, pellet was air dried for 20-30 min at RT and dissolved in nuclease-free water
    4. DNA precipitation
    5. A microtipful cells of bacterial strain from appropriate medium was resuspended in 20 μl sterile water and incubated at 98°C for 10 min for cell lysis. 2 μl of heat-lysed cell suspension was used as template in 25 μl PCR reaction
    6. Xanthomonasand E.colicolony PCR
    1. To perform restriction digestion of plasmid DNA and PCR-amplified DNA products, restriction enzymes were procured from NEW ENGLAND Biolabs(NEB). Restriction digestion was set in 50 μl reaction volume with appropriate buffer and 1X BSA. For ligation of DNA fragments obtained after restriction digestion, T4 DNA Ligase enzyme (NEB, M0202M) was used. All ligation reactions were set in 20 μl reaction volume containing 1X ligase buffer, 3-10 units of DNA ligase enzyme and vector to insert molar ratio of 1:3. The ligation mixture waseitherincubated at 16°C for 16h or at room temperature for 2-3 h. Post incubation, ligation reaction was inhibited by heatingtubes at 65°C for 15-20 min.2-5 μl of ligation mixture was used to transform ultra-competent E. coliDH5αcells
    2. Restriction digestion and ligation
    3. To perform restriction digestion of plasmid DNA and PCR-amplified DNA products, restriction enzymes were procured from NEW ENGLAND Biolabs(NEB). Restriction digestion was set in 50 μl reaction volume with appropriate buffer and 1X BSA. For ligation of DNA fragments obtained after restriction digestion, T4 DNA Ligase enzyme (NEB, M0202M) was used. All ligation reactions were set in 20 μl reaction volume containing 1X ligase buffer, 3-10 units of DNA ligase enzyme and vector to insert molar ratio of 1:3. The ligation mixture waseitherincubated at 16°C for 16h or at room temperature for 2-3 h. Post incubation, ligation reaction was inhibited by heatingtubes at 65°C for 15-20 min.2-5 μl of ligation mixture was used to transform ultra-competent E. coliDH5αcells
    4. Restriction digestion and ligation
    1. were mixed or shaken every 15 min during the incubation as to keep them in suspension. At the end of the incubation, cells were washedagain with 800 μLof rinse bufferby centrifugation at 500 x gfor 6 min and the supernatant was aspirated. BrdU incorporation was detected by adding 100 μLof antibody staining solution containing 5 μLAlexa488 dye labeled anti-Brdu antibody with 95 μLof rinse buffer(1:20 dilution), and the cell suspension was incubated for 30 min at room temperature in the dark.At the end 350 μLof PI staining buffer was added to each sample and incubated for an additional 30 min at room temperature in the dark. Cells were analyzed forthe presence of DSBs by flow cytometry on a FACS ARIA instrument (BD). Viable cells were analyzed for the presence of DNA DSBs by excluding the hypodiploid (<G0/G1)population, using FACS DIVA software (BD). Medianfluorescence values of the treated cells were plotted as a fold difference over untreated controls, using GraphPad Prism 5
    2. Cells were grown in 35mm dishes at 30% initial confluence. At 60% confluence, cells were treated with 0.2 mMhydroxyurea for 12 h. After treatment,media containing drug was removed and fresh media was added for recovery of the cells from genotoxic stress.DNA DSBs were monitored during the treatment period and recovery period of 3, 6, 9 and 12 h. At each time point cells were harvested and fixed using 70% icecold ethanol by gentle vortexing at very low speed and kept overnight at -20ºC. A TUNEL assay to detect DSBs was conducted using Apo-DirectTunel assay kit (A35127, Invitrogen). After overnight fixation, cells were washed with 800 μLof wash buffer, and 50 μLof DNA labeling solution [10 μL reaction buffer, 0.75 μL of TdT enzyme, 8 μL of BrdUTP and 31.25 μLof dH2O (Sigma)]was added to each sample, incubated at 37ºC for 4 h. Samples
    3. Detecting DNA DSBs by TUNEL assay